Origin IGS: cgaaaaaagtctcgaagcggcctcagccttgtcagccgttgctcccgtcgtaacaatcaggctttccccgcccgcttgctgaactttgcctaaaagatcaccaaaaagaatacgttcctttacaaaacgtgtattactctaccatacggtttcgtgtgcaaccaatacaccctctacactcctacgcatcgatacgtaattttcatttttcgttgtcataactcccttcatttaaactttatatacaacgatccgggaataaaaaaatttaacaaaactcactctttttatctttcttacacaacaagatttgattctatccctgtcagaacgataaaacgccctgcccaaagagaaaaatgccatggcagaacgaaaaaacgctccgtcagaggcaaaaaaagccttccaccttctcttttta .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 taaaaagagaaggtggaaggctttttttgcctctgacggagcgttttttcgttctgccatggcatttttctctttgggcagggcgttttatcgttctgacagggatagaatcaaatcttgttgtgtaagaaagataaaaagagtgagttttgttaaatttttttattcccggatcgttgtatataaagtttaaatgaagggagttatgacaacgaaaaatgaaaattacgtatcgatgcgtaggagtgtagagggtgtattggttgcacacgaaaccgtatggtagagtaatacacgttttgtaaaggaacgtattctttttggtgatcttttaggcaaagttcagcaagcgggcggggaaagcctgattgttacgacgggagcaacggctgacaaggctgaggccgcttcgagacttttttcg Mask Tandem Repeat Region ================================================ cgaaaaaagtctcgaagcggcctcagccttgtcagccgttgctcccgtcgtaacaatcaggctttccccgcccgcttgctgaactttgcctaaaagatcaccaaaaagaatacgttcctttacaaaacgtgtattactctaccatacggtttcgtgtgcaaccaatacaccctctacactcctacgcatcgatacgtaattttcatttttcgttgtcataactcccttcatttaaactttatatacaacgatccgggaataaaaaaatttaacaaaactcactctttttatctttcttacacaacaagatttgattctatccctgtcagaacgataaaacgccctgcccaaagagaaaaatgccatggcagaacgaaaaaacgctccgtcagaggcaaaaaaagccttccaccttctcttttta Find is-nt database================================================ Query_seq: TF0993:TF0994|TF0993:TF0994:hypothetical protein:maltose O-acetyltransferase:->->:1048843..1049266 424 cgaaaaaagtctcgaagcggcctcagccttgtcagccgttgctcccgtcgtaacaatcaggctttccccgcccgcttgctgaactttgcctaaaagatcaccaaaaagaatacgttcctttacaaaacgtgtattactctaccatacggtttcgtgtgcaaccaatacaccctctacactcctacgcatcgatacgtaattttcatttttcgttgtcataactcccttcatttaaactttatatacaacgatccgggaataaaaaaatttaacaaaactcactctttttatctttcttacacaacaagatttgattctatccctgtcagaacgataaaacgccctgcccaaagagaaaaatgccatggcagaacgaaaaaacgctccgtcagaggcaaaaaaagccttccaccttctcttttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TF0993:TF0994|TF0993:TF0994:hypothetical protein:maltose O-acetyltransferase:->->:1048843..1049266 424 cgaaaaaagtctcgaagcggcctcagccttgtcagccgttgctcccgtcgtaacaatcaggctttccccgcccgcttgctgaactttgcctaaaagatcaccaaaaagaatacgttcctttacaaaacgtgtattactctaccatacggtttcgtgtgcaaccaatacaccctctacactcctacgcatcgatacgtaattttcatttttcgttgtcataactcccttcatttaaactttatatacaacgatccgggaataaaaaaatttaacaaaactcactctttttatctttcttacacaacaagatttgattctatccctgtcagaacgataaaacgccctgcccaaagagaaaaatgccatggcagaacgaaaaaacgctccgtcagaggcaaaaaaagccttccaccttctcttttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TF0993:TF0994|TF0993:TF0994:hypothetical protein:maltose O-acetyltransferase:->->:1048843..1049266 424 cgaaaaaagtctcgaagcggcctcagccttgtcagccgttgctcccgtcgtaacaatcaggctttccccgcccgcttgctgaactttgcctaaaagatcaccaaaaagaatacgttcctttacaaaacgtgtattactctaccatacggtttcgtgtgcaaccaatacaccctctacactcctacgcatcgatacgtaattttcatttttcgttgtcataactcccttcatttaaactttatatacaacgatccgggaataaaaaaatttaacaaaactcactctttttatctttcttacacaacaagatttgattctatccctgtcagaacgataaaacgccctgcccaaagagaaaaatgccatggcagaacgaaaaaacgctccgtcagaggcaaaaaaagccttccaccttctcttttta Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 cgaaaaaagtctcgaagcggcctcagccttgtcagccgttgctcccgtcgtaacaatcaggctttccccgcccgcttgctgaactttgcctaaaagatcaccaaaaagaatacgttcctttacaaaacgtgtattactctaccatacggtttcgtgtgcaaccaatacaccctctacactcctacgcatcgatacgtaattttcatttttcgttgtcataactcccttcatttaaactttatatacaacgatccgggaataaaaaaatttaacaaaactcactctttttatctttcttacacaacaagatttgattctatccctgtcagaacgataaaacgccctgcccaaagagaaaaatgccatggcagaacgaaaaaacgctccgtcagaggcaaaaaaagccttccaccttctcttttta Predict ORF larger than 30AA ================================================ Protein_Len: 37 Strand: + Start: 86 End: 196 ..................................................................................... M P K R S P K R I R S F T K R V L L Y H T V S C A T N T P S T L L R I D T .................................................................................................................................................................................................................................... Protein_Len: 30 Strand: + Start: 129 End: 218 ................................................................................................................................ M Y Y S T I R F R V Q P I H P L H S Y A S I R N F H F S L S .............................................................................................................................................................................................................. Protein_Len: 60 Strand: + Start: 97 End: 423 ................................................................................................ M T K K N T F L Y K T C I T L P Y G F V C N Q Y T L Y T P T H R Y V I F I F R C H N S L H L N F I Y N D P G I K K F N K . Protein_Len: 33 Strand: - Start: 300 End: 398 ........................................................................................................................................................................................................................................................................................................... V V L N S E I G T L V I F R G A W L S F H W P L V F F R E T L P M .......................... Protein_Len: 44 Strand: - Start: 235 End: 366 .......................................................................................................................................................................................................................................... V K Y V V I R S Y F F K V F S V R K I K R V C C S K I R D R D S R Y F A R G L S F F A M .......................................................... Protein_Len: 30 Strand: - Start: 142 End: 231 ............................................................................................................................................. W V T E H A V L V G E V S R R M S V Y N E N K T T M V G K M ................................................................................................................................................................................................. Protein_Len: 37 Strand: - Start: 1 End: 111 S F L R S A A E A K D A T A G T T V I L S E G G A Q Q V K G L L D G F L M ......................................................................................................................................................................................................................................................................................................................... cgaaaaaagtctcgaagcggcctcagccttgtcagccgttgctcccgtcgtaacaatcaggctttccccgcccgcttgctgaactttgcctaaaagatcaccaaaaagaatacgttcctttacaaaacgtgtattactctaccatacggtttcgtgtgcaaccaatacaccctctacactcctacgcatcgatacgtaattttcatttttcgttgtcataactcccttcatttaaactttatatacaacgatccgggaataaaaaaatttaacaaaactcactctttttatctttcttacacaacaagatttgattctatccctgtcagaacgataaaacgccctgcccaaagagaaaaatgccatggcagaacgaaaaaacgctccgtcagaggcaaaaaaagccttccaccttctcttttta Predict Promoter with matrix: RpoD-15 score > 80================================================ Predict Promoter with matrix: RpoD-16 score > 80================================================ Predict Promoter with matrix: RpoD-17 score > 80================================================ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ cgaaaaaagtctcgaagcggcctcagccttgtcagccgttgctcccgtcgtaacaatcaggctttccccgcccgcttgctgaactttgcctaaaagatcaccaaaaagaatacgttcctttacaaaacgtgtattactctaccatacggtttcgtgtgcaaccaatacaccctctacactcctacgcatcgatacgtaattttcatttttcgttgtcataactcccttcatttaaactttatatacaacgatccgggaataaaaaaatttaacaaaactcactctttttatctttcttacacaacaagatttgattctatccctgtcagaacgataaaacgccctgcccaaagagaaaaatgccatggcagaacgaaaaaacgctccgtcagaggcaaaaaaagccttccaccttctcttttta Predict TransTerm conf > 70================================================ TransTerm Strand: + Conf: 45 HP_score: -2.0 Tail_Score: -3.27022 Start: 121 End: 133 Full_Region: AAGAATACGTTCCTT TACA AAACG TGTA TTACTCTACCATACG ........................................................................................................................TACAAAACGTGTA................................................................................................................................................................................................................................................................................................... Find igs database================================================ Query_seq: TF0993:TF0994|TF0993:TF0994:hypothetical protein:maltose O-acetyltransferase:->->:1048843..1049266 424 cgaaaaaagtctcgaagcggcctcagccttgtcagccgttgctcccgtcgtaacaatcaggctttccccgcccgcttgctgaactttgcctaaaagatcaccaaaaagaatacgttcctttacaaaacgtgtattactctaccatacggtttcgtgtgcaaccaatacaccctctacactcctacgcatcgatacgtaattttcatttttcgttgtcataactcccttcatttaaactttatatacaacgatccgggaataaaaaaatttaacaaaactcactctttttatctttcttacacaacaagatttgattctatccctgtcagaacgataaaacgccctgcccaaagagaaaaatgccatggcagaacgaaaaaacgctccgtcagaggcaaaaaaagccttccaccttctcttttta Intra-Species Hit: Count: 1 Min: 1 Max: 424 Len: 424 Subject: tfor_TF0993_TF0994|hypothetical protein:maltose O-acetyltransferase|POSITIVE:POSITIVE|[1048843, 1049266]|424 HSP 1 e-value: 0.0 bit: 757.0 Len: 424 Query Start:1 Query End:424 Subject Strand: POSITIVE Subject Start: 1 Subject End: 424 cgaaaaaagtctcgaagcggcctcagccttgtcagccgttgctcccgtcgtaacaatcaggctttccccgcccgcttgctgaactttgcctaaaagatcaccaaaaagaatacgttcctttacaaaacgtgtattactctaccatacggtttcgtgtgcaaccaatacaccctctacactcctacgcatcgatacgtaattttcatttttcgttgtcataactcccttcatttaaactttatatacaacgatccgggaatnnnnnnntttaacaaaactcactctttttatctttcttacacaacaagatttgattctatccctgtcagaacgataaaacgccctgcccaaagagaaaaatgccatggcagaacgaaaaaacgctccgtcagaggcnnnnnnngccttccaccttctcttttta cgaaaaaagtctcgaagcggcctcagccttgtcagccgttgctcccgtcgtaacaatcaggctttccccgcccgcttgctgaactttgcctaaaagatcaccaaaaagaatacgttcctttacaaaacgtgtattactctaccatacggtttcgtgtgcaaccaatacaccctctacactcctacgcatcgatacgtaattttcatttttcgttgtcataactcccttcatttaaactttatatacaacgatccgggaataaaaaaatttaacaaaactcactctttttatctttcttacacaacaagatttgattctatccctgtcagaacgataaaacgccctgcccaaagagaaaaatgccatggcagaacgaaaaaacgctccgtcagaggcaaaaaaagccttccaccttctcttttta Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CGAAAAAAGUCUCGAAGCGGCCUCAGCCUUGUCAGCCGUUGCUCCCGUCGUAACAAUCAGGCUUUCCCCGCCCGCUUGCUGAACUUUGCCUAAAAGAUCACCAAAAAGAAUACGUUCCUUUACAAAACGUGUAUUACUCUACCAUACGGUUUCGUGUGCAACCAAUACACCCUCUACACUCCUACGCAUCGAUACGUAAUUUUCAUUUUUCGUUGUCAUAACUCCCUUCAUUUAAACUUUAUAUACAACGAUCCGGGAAUAAAAAAAUUUAACAAAACUCACUCUUUUUAUCUUUCUUACACAACAAGAUUUGAUUCUAUCCCUGUCAGAACGAUAAAACGCCCUGCCCAAAGAGAAAAAUGCCAUGGCAGAACGAAAAAACGCUCCGUCAGAGGCAAAAAAAGCCUUCCACCUUCUCUUUUUA .(((((..((.((((.((((....(((((.(......(((((.......)))))...))))))....))))..((.((.(((.((((.....)))).))).))...(((....((......)).....(((((((.......((((((....)))))).....)))))))..)))..........)).)))).))....))))).....(((((((.(((.....................))))))))))...(((..((((....))))..............(((((((.((((.(((.....(((......))).....))).)))).)))))))..))).....((((((((........((((.((.((......)).)).))))(((((.......))))).....))))))))... (-78.30) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAAAAGAGAAGGUGGAAGGCUUUUUUUGCCUCUGACGGAGCGUUUUUUCGUUCUGCCAUGGCAUUUUUCUCUUUGGGCAGGGCGUUUUAUCGUUCUGACAGGGAUAGAAUCAAAUCUUGUUGUGUAAGAAAGAUAAAAAGAGUGAGUUUUGUUAAAUUUUUUUAUUCCCGGAUCGUUGUAUAUAAAGUUUAAAUGAAGGGAGUUAUGACAACGAAAAAUGAAAAUUACGUAUCGAUGCGUAGGAGUGUAGAGGGUGUAUUGGUUGCACACGAAACCGUAUGGUAGAGUAAUACACGUUUUGUAAAGGAACGUAUUCUUUUUGGUGAUCUUUUAGGCAAAGUUCAGCAAGCGGGCGGGGAAAGCCUGAUUGUUACGACGGGAGCAACGGCUGACAAGGCUGAGGCCGCUUCGAGACUUUUUUCG ......((((((.....((((((((((((((((((.(((((((......(((((((((..((.........))...)))))))))......))))))).)))..............((((((((((..(((((((((((((((((.((((..(((........((((((....(((((((.(((((..(((.......)))..))))))))))))...........((((((....)))))))))))).((((.((((((((.((((..(((....)))...))))..)))))))).)))).)))..)))).))))))))))....)))))))..))).....))))))).)))))))))))))))....(((.(((.(.(.((..(((((.....)))))..))).).))).))).)))))). (-127.10) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 442 49 8 56 2 tfor:TF2704|5end_ribonuclease_HII_2876242..2876472_POSITIVE 428 97 57 158 110 tfor:TF2487|5end_transposase_2663010..2663240_POSITIVE 420 79 32 71 3 tfor:TF2882|5end_conserved_hypothetical_protein_3073419..3073649_POSITIVE 409 76 32 211 156 tfor:TF3022|5end_chorismate_synthase_3246136..3246366_POSITIVE 408 78 37 73 28 tfor:TF2833|5end_lipid_A_disaccharide_synthase_3023973..3024203_POSITIVE 408 79 35 76 29 tfor:TF0001|5end_hypothetical_protein_-116..114_POSITIVE 406 51 11 45 8 tfor:TF1591|5end_surface_antigen_BspA_1706387..1706617_POSITIVE 403 70 24 146 95 tfor:TF0038|5end_conserved_hypothetical_protein_39907..40137_POSITIVE 387 80 31 184 134 tfor:TF2601|5end_conserved_hypothetical_protein_2774721..2774951_POSITIVE 387 79 37 219 169 tfor:TF2120|5end_holliday_junction_endonuclease_2292108..2292338_POSITIVE 386 49 1 68 19 tfor:TF2439|5end_conserved_hypothetical_protein_2616380..2616610_POSITIVE 383 79 36 228 171 tfor:TF3152|5end_hypothetical_protein_3386690..3386920_POSITIVE 380 79 36 44 5 tfor:TF0471|5end_conserved_hypothetical_protein_487516..487746_POSITIVE 377 377 341 73 36 tfor:TF2256|5end_transfer_region-related_protein,_TraI_2427908..2428138_POSITIVE 374 60 12 76 25 tfor:TF2766|5end_shikimate_kinase_2951619..2951849_POSITIVE 374 50 12 66 10 tfor:TF2229.1|5end_rteR_regulatory_ortholog_(with_internal_stop)_2399454..2399684_POSITIVE 374 80 34 57 2 tfor:TF0851|5end_helicase_SNF2_family_899486..899716_POSITIVE 373 90 42 53 1 tfor:TF2876|5end_cytosine_deaminase_3065144..3065374_POSITIVE 373 51 12 45 6 tfor:TF0461|5end_ATP:cob(I)alamin_adenosyltransferase_476990..477220_POSITIVE 372 73 36 213 166 tfor:TF2561|5end_50S_ribosomal_protein_L16_2738693..2738923_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 452 50 9 46 4 tfor:TF0886|3end_conjugative_transposon_protein_fragment_938152..938302_POSITIVE 438 49 8 51 9 tfor:TF2703|3end_conserved_hypothetical_protein_2876317..2876467_POSITIVE 406 80 31 150 93 tfor:TF1443|3end_hypothetical_protein_1528203..1528353_POSITIVE 403 70 24 150 99 tfor:TF0037|3end_sialic_acid-specific_9-O-acetylesterase_39991..40141_POSITIVE 387 80 31 92 42 tfor:TF2600|3end_ribose-phosphate_pyrophosphokinase_2774709..2774859_POSITIVE 377 377 341 46 9 tfor:TF2255|3end_transfer_region-related_protein,_TraH_2427961..2428111_POSITIVE 373 90 42 53 1 tfor:TF2874|3end_conserved_hypothetical_protein_3065224..3065374_POSITIVE 373 51 12 45 6 tfor:TF0460|3end_hypothetical_protein_477070..477220_POSITIVE 363 50 2 133 70 tfor:TF0991|3end_probable_NAD(FAD)-dependent_dehydrogenase_1048334..1048484_POSITIVE 361 52 11 147 103 tfor:TF3021|3end_FKBP-type_peptidyl-prolyl_cis-trans_isomerase_3246194..3246344_POSITIVE 361 59 16 109 57 tfor:TF1944|3end_conserved_hypothetical_protein_2093309..2093459_POSITIVE 360 73 31 151 119 tfor:TF2795|3end_hypothetical_protein_2980909..2981059_POSITIVE 359 80 31 83 24 tfor:TF0599|3end_hypothetical_protein_630130..630280_POSITIVE 358 90 43 77 13 tfor:TF2366|3end_conserved_hypothetical_protein_2531892..2532042_POSITIVE 354 50 1 75 28 tfor:TF0010|3end_conserved_hypothetical_protein_4790..4940_POSITIVE 353 48 7 56 6 tfor:TF2631|3end_conserved_hypothetical_protein_2802088..2802238_POSITIVE 353 60 11 91 35 tfor:TF1927|3end_RNA_polymerase_sigma-70_factor,_ECF_subfamily_2075602..2075752_POSITIVE 352 69 23 128 80 tfor:TF2816|3end_hypothetical_protein_3007184..3007334_POSITIVE 351 396 351 147 96 tfor:TF1946|3end_membrane_protein;_spore_maturation-like_protein_2095601..2095751_POSITIVE 351 70 23 66 7 tfor:TF1683|3end_conserved_hypothetical_protein_1796511..1796661_POSITIVE